3D-scanning technology is changing the way researchers investigate and conserve precious artifacts and major scientific finds.

One morning in November 2011, trucks were roaring down the Pan-American Highway, carrying loads of ore from mines in the Atacama Desert to the port town of Caldera, Chile. The trucks screamed past a young goateed American paleontologist named Nicholas Pyenson, who was standing at the side of the road, gazing at a 250-meter-long strip of sandstone that construction workers had cleared in preparation for building new lanes.

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Pyenson, the curator of fossil marine mammals at the Smithsonian Institution, spends much of his time searching for fossils of whales. For over a year his Chilean colleague Mario Suárez had been nagging him to come to see whale fossils that had been exposed as construction workers widened the highway. Pyenson envisioned a few skull fragments wedged in a road cut—a very low priority. After completing his work at another fossil site in Chile, Pyenson finally agreed to go see the remains. And standing by the highway, he realized why Suárez had been so insistent. The road crew had uncovered not just a few whale bones but an entire whale graveyard. At least 40 prehistoric whales, some 30 feet long, were spread out before him. It would turn out to be the densest collection of fossil whales discovered anywhere in the world.

Whales may be some of the most remarkable animals in the history of life—they evolved, after all, from deerlike mammals on land and became top predators of the sea. But their fossils can be a nightmare for paleontologists. "I wouldn't wish a whale fossil on anyone," Pyenson says. "Especially not 40."

Finding out what killed these creatures would require a huge amount of time and resources. A team of paleontologists would need to document each fossil while it was still in the ground in order to gather clues to the environment in which the whales had died. But there simply was no time to undertake an on-site study of their placement because the graveyard had been found in the middle of a construction project. Pyenson got to the site, within the town limits of Caldera, with the clock already ticking. There was only a month left in the federally mandated time allotted to researchers seeking to mine fossils and relics from the construction site.

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Pyenson found a solution to his quandary—one that offers a glimpse into the future of paleontology. He flew home to Washington, D.C., and returned to Chile two weeks later with Vincent Rossi and Adam Metallo, the two young men who run the Smithsonian's 3D-digitization project. Instead of digging tools and plaster, the pair took laser scanners and cameras to the site.

The laser cowboys, as Pyenson dubbed them during the Caldera work, set up a tent over the fossils and worked for six days straight, 20 hours a day, to capture billions of pixels of data. Back at the Smithsonian, Pyenson and his colleagues used the data to re-create the site on their computers, exploring the virtual graveyard to figure out how the animals died.

And they're able to share this knowledge in a new way—by printing high-quality replicas of the fossils. In a few months the Smithsonian is slated to unveil a 30-foot-long skeleton of one of the Caldera whales in the National Museum of Natural History. "It's the largest 3D print of its kind in the world," Pyenson says.

The display is a public reminder of how the ongoing revolution in digitization is changing disciplines in and out of science. The ability to preserve detailed schematic information has always been important—think of sketches and blueprints—but modern scanning technology can capture exact details for later fabrication and analysis. Today, using scanning technology, engineers in different parts of the world can collaborate in real time on ever-changing vehicle designs, customers can create parts on demand from supplier schematics, and surgeons can make detailed pre-op models of individual patients.

For the Smithsonian, laser scans provide a means to share the institution's immense collection with the public. In 2013 the laser cowboys launched an ambitious campaign to catalog high-resolution scans of items throughout the Smithsonian's museums—including some of Pyenson's whale fossils—and make them navigable online. "You just say, it's all free," Pyenson says. "Here's the digital avatar. Researchers, 10-year-old kids, artists—have at it."

Smithsonian Institution

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A crew of specialists use laser technology to investigate a rare fossil find in Chile. (Photograph by Smithsonian Institution)

Scanning and 3D printing in paleontology build on 350 years of visualization tradition. In the 1660s anatomist Nicolas Steno astonished Europe's natural philosophers by publishing images of triangular rocks known as tongue stones, which he depicted next to the teeth of sharks. Anyone looking at the engravings could see that the tongue stones were the mineralized remains of long-dead sharks.

Later generations of paleontologists took advantage of every advance in visual technology to display their fossils in better ways—from copper-plate engravings to color photographs. But these two-dimensional views of fossils left out more than they left in. To study a species, paleontologists had to travel from museum to museum to examine fossils in person.

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In the late 1990s Tim Rowe, a paleontologist at the University of Texas, pioneered a new way to see fossils—with the help of X-rays. Rowe began to put fossils in CT scanners, which could capture their 3D structures. Rowe's scanners could snoop inside as well, mapping brain cases, sinuses, and other hidden anatomical features.

More than 150 paleontologists have shipped fossils to Rowe for scanning, and he's supplied them with pictures of hundreds of slices of the material, which can be converted into 3D animations. Rowe also puts the data on his DigiMorph website, where anyone can download it. Paleontologists can analyze scans for their research or print out replicas of fossils so that they can have the satisfaction of turning the bones over in their hands.

Once paleontologists create 3D scans of fossils, they can use them to reconstruct an animal's life history. Larry Witmer and his colleagues at Ohio University, for example, use scans to get a better idea of how dinosaurs moved. Recently they investigated the huge predator Allosaurus to understand how it ate its prey.

Witmer and his team started their study by scanning a 5-foot-long Allosaurus skull and the neck bones from a 150-million-year-old fossil. They then identified the crests and knobs on the bones where muscles and tendons were once attached. Based on studies of living dinosaur relatives, such as alligators and birds, they could estimate the size and shape of those pieces of soft tissue. And with engineering software they could then calculate the forces Allosaurus was able to generate, and how it moved.

The scientists used this information to create an animation of Allosaurus moving its head in different directions. They found that the animal had an anatomy profoundly different from that of other predatory dinosaurs. A large muscle that ran from its neck to its head allowed it to generate tremendous upward force. Tyrannosaurus rex, by contrast, generated side-to-side forces, indicating that it shook its head while gripping its prey.

In Witmer's animation, Allosaurus moves in a very different way. It looks more like a falcon digging into its prey. To feed, a falcon contracts the same type of neck muscle, yanking up its beak to rip a bite of flesh. Given that Allosaurus and other ground-running dinosaurs were related to birds—and even had feathers—the similarity probably isn't coincidental. But it's still surreal to imagine a 25-foot-long, ground-running dinosaur tugging, falcon-like, at its victim's body.

Ian Allen

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Our own evolution is also becoming clearer, thanks to 3D visualization. It's rare for scientists to find an intact fossil of an ancient relative of ours. Instead, human ancestors often leave behind mineralized bones that have shattered into dozens or hundreds of fragments. Early generations of paleontologists spent years piecing together these hominid jigsaw puzzles by hand. Now they can scan the fragments and manipulate them in the virtual space of a computer. By applying complex geometric equations to the shapes, scientists can build more accurate reconstructions of the original bones, helping them tackle all sorts of questions about human evolution, from how our ancestors stood on two legs to how they split apart from Neanderthals.

While a single fossil can tell paleontologists a lot, no animal lived on its own. Paleontologists can look at how fossils formed to get clues to the web of life that supported them millions of years ago. And when Pyenson examined the scan of the Caldera whale site, he learned just how powerful 3D visualization is for resurrecting entire ecosystems.

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Inside the long, low tent that Pyenson and his colleagues pitched over the fossils, Rossi and Metallo set up their equipment, taking photographs across the entire site with a Canon 5D. Then, using a handheld laser, they maneuvered around individual fossils. Both of these approaches created vast clouds of data points, which Rossi and Metallo stored on computers.

Back at the Smithsonian the team began reconstructing the site from their data. First, they processed high-resolution topographical scans of the individual fossils. By patching these together with photographs, they created a comprehensive 3D representation of the site. In places, they zoomed in on details smaller than a millimeter.

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The data revealed remains of an abundance of other big animals, such as aquatic sloths, swordfish, and seals. "Here's a scientific question: How did all these things get here?" Pyenson asks.

The more Pyenson studied the fossils, the more they seemed like victims of a massacre—making Pyenson himself a kind of paleontological version of a forensic criminologist. The data from the site allowed him to explore the crime scene. "If we didn't do what we did, we would have just gotten the bag of bones from the murder case," Pyenson says. "Having the CSI-type 3D preservation can tell you so much more."

Pyenson and his colleagues started to gather clues. They observed that the skeletons had fossilized intact, meaning that they hadn't been ripped apart by predators. Among the fossils were three whales of the same species huddled together, possibly a family that had died at once. Pyenson also noticed that the fossils formed four separate layers arranged on top of each other in a stack 30 feet high. That meant a lot of big animals had died in the same place, again and again, over a span of about 14,000 years between 6 million and 9 million years ago. The final clue was not among the fossils but sprinkled on top of them. Pyenson and his colleagues observed that the fossils were coated with a mat of algae. "The number of explanations for that is vanishingly small," Pyenson says. "It comes down to red tides."

From time to time, the conditions in the ocean line up such that the populations of some species of algae explode. The algae produce toxins that can cause deadly seizures in fish and marine mammals. There are almost no reports of whales dying in red tides, but the few that do exist paint a picture that looks a lot like the 3D digitization of the Caldera site. Red tides also tend to strike the same places again and again, which could account for the layers of fossils. "The explanation works because it shows how many large individuals can be killed in the same way," Pyenson says.

Before 3D digitization, it would have been impossible for Pyenson to come to this conclusion so quickly after first laying eyes on the Caldera site. Bones from a site can be preserved in temporary plaster jackets—and at Caldera, some were—but it could be decades before they are prepared for analysis. In the meantime, using scans, there is still much more for scientists to explore. For example, the whale replica that is to be mounted on the wall of the Smithsonian may be a new species. "There are going to be future dissertations on these whales," Pyenson says.

That's a profound change from the way paleontology has been done up till now. A graduate student who wanted to write a dissertation on the Caldera whales would have had to travel to look at the skeletons. Pyenson has now offered future generations of scientists a way to examine bones online. And if they need to hold a bone in their hands to understand the anatomy of a species, they can print out a nearly perfect copy.

But for scientists to gain that access, the Smithsonian will need to make the data available through portals that allow for easy navigation. "It changes the game for museums," Pyenson says. "I think we need to archive digital data."

Rossi and Metallo, the laser cowboys, are transforming the Smithsonian's collection into 3D avatars. They've created a browser plug-in that allows anyone with an Internet connection to zoom in on a Smithsonian object—fossil or otherwise—down to submillimeter scale.

The technology promises to be a boon to many fields of study. Art experts will be able to inspect the Smithsonian's ancient sculptures, while historians will be able to read inscriptions on artifacts. And as part of a pilot project, Rossi and Metallo used lasers to scan a fragile toothed whale skull Pyenson has been studying, as well as the woolly mammoth skeleton on display in the National Museum of Natural History.

While Pyenson can see great things ahead for paleontology, what gets him most excited is using 3D visualization to take the Smithsonian to the public in a more intimate way—to "make the walls transparent," as he puts it. He can't predict what will happen when the fossils get into the public's hands—to explore, to print out, to experience. "That's the unforeseen consequence," Pyenson says. "And that's going to be awesome."